miRNA: 3'- caCACCU----UCAGUUCCaCUUcCGCUUG- -5'
miRNA: 3'- caCACC---------------UUCAGUUCCacuUCCGCUUG- -5'
miRNA: 3'- cACACCuUCAguUCCACU----UCCGCUUg -5'
miRNA: 3'- -CACACCUUCAGUUCCACUUCCGCUUG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 11943 | 5' | -50.6 | NC_003278.1 | + | 21247 | 0.66 | 0.804832 |
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Target: 5'- -aGUGGGuugaAGUCGAGGaGGAuGCGGAUg -3' miRNA: 3'- caCACCU----UCAGUUCCaCUUcCGCUUG- -5' |
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| 11943 | 5' | -50.6 | NC_003278.1 | + | 26700 | 0.67 | 0.744377 |
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Target: 5'- -cGUGGuugucgaacuucuucAGGUCGAGGcccAGGCGGGCg -3' miRNA: 3'- caCACC---------------UUCAGUUCCacuUCCGCUUG- -5' |
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| 11943 | 5' | -50.6 | NC_003278.1 | + | 17194 | 0.69 | 0.646722 |
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Target: 5'- cUGUGGuGGUgcGGGUGAagccGGGCGAGg -3' miRNA: 3'- cACACCuUCAguUCCACU----UCCGCUUg -5' |
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| 11943 | 5' | -50.6 | NC_003278.1 | + | 677 | 1.11 | 0.001157 |
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Target: 5'- gGUGUGGAAGUCAAGGUGAAGGCGAACa -3' miRNA: 3'- -CACACCUUCAGUUCCACUUCCGCUUG- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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